1. T. Okada, G. Isacchini, Q. Yu, & O. Hallatschek. (2025). Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series. Proceedings of the National Academy of Sciences, 122(48), e2500663122.

  2. Y. J. Huang, T. Okada and A. Mochizuki, Uncovering Bifurcation Behaviors of Biochemical Reaction Systems from Network Topology, Sci. Rep. 15, 27596 (2025).

  3. M. Honjo, K. Suzuki, J. Katai, Y. Tashiro, T. Aoyagi, T. Hori, T. Okada, Y. Saito and H. Futamata, Stable States of a Microbial Community Are Formed by Dynamic Metabolic Networks with Members Functioning to Achieve Both Robustness and Plasticity, Microbes Environ. 39, ME23091 (2024).

  4. A. Hishida, T. Okada and A. Mochizuki, Patterns of change in regulatory modules of chemical reaction systems induced by network modification, PNAS Nexus 3, pgad441 (2024).

  5. Q. Yu, J. Ascensao, T. Okada, COG-UK consortium, O. Boyd, E. Volz and O. Hallatschek, Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England, PLoS Pathog. (2024).

  6. Y. Yamauchi, A. Hishida, T. Okada and A. Mochizuki, Finding regulatory modules of chemical reaction systems, Phys. Rev. Res. 6, 023150 (2024).

  7. S. Hosoda, H. Iwata, T. Miura, M. Tanabe, T. Okada, A. Mochizuki and M. Sato, BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks, BMC Bioinformatics 25, 297 (2024).

  8. H. Ishizawa, Y. Tashiro, T. Okada, D. Inoue, M. Ike and H. Futamata, Uncovering the causal relationships in plant-microbe ecosystems: A time series analysis of the duckweed cultivation system for biomass production and wastewater treatment, Sci. Total Environ. 957, 177717 (2024).

  9. F. Mori and T. Okada, Information-transfer characteristics in network motifs, Phys. Rev. Res. 5, 013037 (2023).

  10. T. Okada, H. Miyagi, Y. Sako, M. Hiroshima and A. Mochizuki, Origin of diverse phosphorylation patterns in the ERBB system, Biophys. J. 121, 470 (2022).

  11. T. Okada, A. Mochizuki, M. Furuta and J. C. Tsai, Flux-augmented bifurcation analysis in chemical reaction network systems, Phys. Rev. E 103, 062212 (2021).

  12. T. Okada and O. Hallatschek, Dynamic Sampling Bias and Overdispersion Induced by Skewed Offspring Distributions, Genetics 219, iyab135 (2021).

  13. Y. Hirono, T. Okada, H. Miyazaki and Y. Hidaka, Structural reduction of chemical reaction networks based on topology, Phys. Rev. Res. 3, 043123 (2021).

  14. F. Mori and T. Okada, Diagrammatic expansion of information flows in stochastic Boolean networks, Phys. Rev. Res. 2, 043432 (2020).

  15. T. Okada, J. C. Tsai and A. Mochizuki, Structural Bifurcation Analysis in Chemical Reaction Networks, Phys. Rev. E 98, 012417 (2018).

  16. A. Ferjani, et al., Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo, Sci. Rep. 8, 14696 (2018).

  17. T. Okada and A. Mochizuki, Sensitivity and Network Topology in Chemical Reaction Systems, Phys. Rev. E 96, 022322 (2017).

  18. T. Okada and A. Mochizuki, Law of localization in chemical reaction networks, Phys. Rev. Lett. 117, 048101 (2016).

  19. Y. Sakatani and T. Okada, Defect branes as Alice strings, JHEP 03, 131 (2015).

  20. Y. Asano, G. Ishiki, T. Okada and S. Shimasaki, Emergent bubbling geometry in the plane wave matrix model, JHEP 05, 075 (2014) [arXiv:1401.5079 [hep-th]].

  21. Y. Asano, G. Ishiki, T. Okada and S. Shimasaki, Exact results for perturbative partition functions of theories with SU(2,4) symmetry, JHEP 02, 148 (2013) [arXiv:1211.0364 [hep-th]].

  22. (Ph.D. Thesis) T. Okada, Matrix Models in String and M-theory and Exact Results, Kyoto University.

  23. H. Kawai and T. Okada, Solving the Naturalness Problem by Baby Universes in the Lorentzian Multiverse, Prog. Theor. Phys. 127, 689 (2012) [arXiv:1110.2303 [hep-th]].

  24. Y. Asano, G. Ishiki, T. Okada and S. Shimasaki, Large-N reduction for N=2 quiver Chern-Simons theories on S^3 and localization in matrix models, Phys. Rev. D 85, 085017 (2012) [arXiv:1203.0559 [hep-th]].

  25. T. Kikuchi, T. Okada and Y. Sakatani, Rotating string in doubled geometry with generalized isometries, Phys. Rev. D 86, 046001 (2012) [arXiv:1205.5549 [hep-th]].

  26. H. Kawai and T. Okada, Asymptotically Vanishing Cosmological Constant in the Multiverse, Int. J. Mod. Phys. A 26, 3107 (2011) [arXiv:1104.1764 [hep-th]].

  27. T. Nishinaka, T. Okada, T. Okazaki and S. Yamaguchi, Evidence for Duality of Conifold from Fundamental String, JHEP 10, 051 (2011) [arXiv:1107.3660 [hep-th]].

  28. M. Asano, J. Hisano, T. Okada and S. Sugiyama, A Realistic Extension of Gauge-Mediated SUSY-Breaking Model with Superconformal Hidden Sector, Phys. Lett. B 673, 146 (2009) [arXiv:0810.4606 [hep-ph]].